Herein is described the use of a collection of 50 breast cancer cell lines to match responses to 77 conventional and experimental therapeutic agents with transcriptional, proteomic and genomic subtypes found in primary tumors. Almost all compounds produced strong differential responses across the cell lines produced responses that were associated with transcriptional and proteomic subtypes and produced responses that were associated with recurrent genome copy number abnormalities. These associations can now be incorporated into clinical trials that test subtype markers and clinical responses simultaneously.

STATEMENT OF GOVERNMENTAL SUPPORT
[0003] This work was supported in part by Contract No. DE-AC02-05CH11231 awarded by the Department of Energy, by Grant Nos. CA058207; U54 CA112970; NHGRI U24, CA126551, and K08CA137153 awarded by the National Cancer Institution of the National Institutes of Health, and by a Work for Others Agreements LB06-002417 with GlaxoSmithKline; LB09005492 with Millennium Pharmaceuticals, Inc.; LB-08004488 with Cytokinetics, Inc.; LB07003395 with Cellgate, Inc. and LB08005005 with Progen Pharmaceuticals Ltd. The government has certain rights in the invention.